movie_alignment_correlation.h

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/***************************************************************************
 *
 * Authors:    Carlos Oscar Sanchez Sorzano coss@cnb.csic.es
 *             David Strelak (davidstrelak@gmail.com)
 *
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/

#ifndef _PROG_MOVIE_ALIGNMENT_CORRELATION
#define _PROG_MOVIE_ALIGNMENT_CORRELATION

#include "data/filters.h"
#include "core/xmipp_fftw.h"
#include "reconstruction/movie_alignment_correlation_base.h"

template<typename T>
class ProgMovieAlignmentCorrelation: public AProgMovieAlignmentCorrelation<T> {
public:
    void defineParams() override;
    void readParams() override;
private:
    void loadData(const MetaData& movie, const Image<T>& dark,
            const Image<T>& igain);

    void computeShifts(size_t N, const Matrix1D<T>& bX, const Matrix1D<T>& bY,
            const Matrix2D<T>& A);

    void applyShiftsComputeAverage(const MetaData& movie, const Image<T>& dark,
            const Image<T>& igain, Image<T>& initialMic, size_t& Ninitial,
            Image<T>& averageMicrograph, size_t& N,
            const AlignmentResult<T> &globAlignment);

    void applyShiftsComputeAverage(
                const MetaData& movie, const Image<T>& dark, const Image<T>& igain,
                Image<T>& initialMic, size_t& Ninitial, Image<T>& averageMicrograph,
                size_t& N, const LocalAlignmentResult<T> &alignment);

    AlignmentResult<T> computeGlobalAlignment(const MetaData &movie,
            const Image<T> &dark,
            const Image<T> &igain);

    void releaseAll() {
        for (auto f : frameFourier) {
            delete f;
        }
        frameFourier.clear();
    };

    LocalAlignmentResult<T> computeLocalAlignment(const MetaData &movie,
            const Image<T> &dark, const Image<T> &igain,
            const AlignmentResult<T> &globAlignment);
private:
    std::vector<MultidimArray<std::complex<T> > *> frameFourier;

    int newXdim;
    int newYdim;

    float sizeFactor;
};
#endif